Multiple Bennett acceptance ratio made easy for replica exchange simulations

2013 ◽  
Vol 139 (12) ◽  
pp. 124105 ◽  
Author(s):  
Piero Procacci
Keyword(s):  
Replica Exchange ◽  
Acceptance Ratio ◽  
Bennett Acceptance Ratio

scholarly journals Multiensemble Markov models of molecular thermodynamics and kinetics

2016 ◽  
Vol 113 (23) ◽  
pp. E3221-E3230 ◽  
Author(s):  
Hao Wu ◽  
Fabian Paul ◽  
Christoph Wehmeyer ◽  
Frank Noé
Keyword(s):  
Detailed Balance ◽  
Rare Event ◽  
Umbrella Sampling ◽  
High Dimensional ◽  
Acceptance Ratio ◽  
Markov State ◽  
Markov State Models ◽  
Bennett Acceptance Ratio ◽  
Special Cases ◽  
State Models

We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models—clustering of high-dimensional spaces and modeling of complex many-state systems—with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein–ligand binding model.

scholarly journals Building a Macro-mixing Dual-basin Go Model using the Multistate Bennett Acceptance Ratio

2020 ◽  
Vol 118 (3) ◽  
pp. 179a
Author(s):  
Ai Shinobu ◽  
Chigusa Kobayashi ◽  
Yasuhiro Matsunaga ◽  
Yuji Sugita
Keyword(s):  
Acceptance Ratio ◽  
Bennett Acceptance Ratio ◽  
Go Model

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification

2018 ◽  
Vol 20 (3) ◽  
pp. 2009-2021 ◽  
Author(s):  
Xiaohui Wang ◽  
Xingzhao Tu ◽  
John Z. H. Zhang ◽  
Zhaoxi Sun
Keyword(s):  
Adaptive Sampling ◽  
Current Work ◽  
Variance Minimization ◽  
Acceptance Ratio ◽  
Bennett Acceptance Ratio ◽  
Sampling Regime

Following the previously proposed equilibrate-state sampling based adaptive sampling regime Optimum Bennett Acceptance Ratio (OBAR), we introduce its nonequilibrium extension, Optimum Crooks’ Equation (OCE) in the current work.

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